[en] SUMMARY: To support small and large-scale genome mining projects, we present Palantir (Post-processing Analysis tooLbox for ANTIsmash Reports), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module, domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. AVAILABILITY: Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Tocquin, Pierre ; Université de Liège - ULiège > Département des sciences de la vie > Physiologie végétale
Cornet, Luc ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Sirjacobs, Damien ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Leclère, Valérie
Pupin, Maude
Jacques, Philippe ; Université de Liège - ULiège > Département GxABT > Microbial, food and biobased technologies
Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Language :
English
Title :
Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects.
Publication date :
2020
Journal title :
Bioinformatics
ISSN :
1367-4803
eISSN :
1367-4811
Volume :
36
Issue :
15
Pages :
4345-4347
Peer reviewed :
Peer reviewed
Name of the research project :
ALIBIOTECH (Hauts-de-France Region)
Funders :
F.R.S.-FNRS - Fonds de la Recherche Scientifique FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture European INTERREG Va SmartBioControl/Bioscreen ULiège - Université de Liège
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